Data Set Used

The analysis of structural and energy features of proteins can be a key to understand how proteins work and interact to each other in cellular reactions. Potential energy is a function of atomic positions in a protein structure. The distributions of energy over each atom in protein structures can be very supportive for the studies of the complex processes… (More)

Analysis of new trends in databases development shows that promising solution in databases gathering a huge quantities of information is approximate retrieval. This work presents the fuzzy queries processing with a special attention to context-dependent and multidimensional membership functions. In the first part, the analysis of occurrence of fuzzy values… (More)

Since protein structure similarity searching is very complex and time-consuming, one of the possible acceleration methods is paral-lelization by distributing the calculation on multiple computers. In the paper, we present a theoretical model of the hierarchical multi-agent system dedicated to the task of protein structure similarity searching. We also show… (More)

Energy features of protein structures can be used to study protein abilities to interact with other biological molecules and possibilities to take part in cellular reactions. In the paper, we present the analysis of the human RAB5A activity with the use of different energy characteristics. Energy characteristics are distributions of potential energy over… (More)

The Energy Distribution Markup Language (EDML) is an XML-based format that we have designed and developed to exchange protein structure energy profiles between many computers and users. Energy profiles that are distributions of various potential energies over consecutive atoms in protein molecular structures can be downloaded from the Energy Distribution… (More)

One of the advantages of using multi-agent systems in solving many problems is their high scalability adequately to the demand for computing power. This important feature underlies our agent-based system for protein structure similarity searching. In this paper, we present the general architecture of the system, implementation details, communication between… (More)